Comments (3)
yarikoptic
commented on July 16, 2024
apptainer/singularity#5408 suggests that we need freshier singularity since we have
$> docker run --privileged --rm -e UID=47521 -e GID=47522 -v /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc:/home/yoh/.tmp/repro-6XkWWkE/ds000003-qc -v /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers:/home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers -v /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers/binds/HOME:/home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers/binds/HOME -w /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc -v /etc/localtime --entrypoint singularity mjtravers/singularity-shim:latest --version
singularity version 3.3.0-1
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yarikoptic
commented on July 16, 2024
damn -- I guess #42 was intended to fix it all but was "forgotten". will get back to it now.
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yarikoptic
commented on July 16, 2024
#42 and followup commits + updated docker build of the repronim/containers should have addressed this issue
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Related Issues (20)
- containers/scripts/singularity_cmd: Argument list too long HOT 2
- rewrite freeze_versions in Python HOT 4
- Add retries for docker hub connections
- Add fMRIprep 22.0.1 HOT 4
- Rewrite create_singularities in Python HOT 4
- Add containers for ABCD apps HOT 2
- Add fmriprep-fake BIDS-App container
- Go through the typical workflow and "relate" to reproman workflow HOT 3
- Expanded version of explanations for typical workflow HOT 1
- MRIQC OOM error causes unhelpful nipype NodeExecutionError HOT 3
- Warning in output: Set MPLCONFIGDIR when running bids-mriqc HOT 4
- JOSS paper
- make "freeze_version" freeze them in the "super-dataset" instead of the ReproNim/containers HOT 6
- Make testing actually test the version of this dataset as provided in PR
- Update walkthrough for the new preferable way of freezing in superds HOT 1
- fmriprep-fake docker image breaks build process HOT 4
- Bind files/directories into containers? HOT 5
- Investigate CDI support
- apptainer, cache write error HOT 2
- Move from travis to github actions HOT 4
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